The male-sterile line has been largely used in the hybrid seed production of pepper, which can effectively improve the efficiency of hybrid seed production. However, the formation mechanism of male sterility in pepper remains unclear. In the present study, we compared the gene expression pattes between pepper cytoplasmic male sterile line 9704A and its maintainer 9704B duringfloral bud development using RNA sequencing technology. A total of 547976 and 2416 Differentially Expressed Genes (DEGs) were identified in the stage S1, S2 and S3, respectively, and more than 70％of the DEGs were down-regulated in the sterile line. Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to further understand the functions of these identified DEGs. The results showed that the DEGs were mainly enriched in pathways of starch and sucrose metabolism, pentose and glucuronate interconversions. A number of genes, such as MS1, PME5, ATPB, and lots of transcription factors were found down-regulated in the sterile line, and we also identified a series of genes with large differences in expression pattes between sterile line and maintainer line. Collectively, ourfindings laid a foundation for further molecular breeding in pepper and provided new insights into its mechanism underlying the male sterility.